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tree-sitter-fastq

tree-sitter-fastq is a parser for the FASTQ file format in genomics and high throughput sequencing. It based on Tree-sitter, which is supported by many text editors. tree-sitter-fastq can be used both as a language grammar in a text editor or as a parser in a programming language supported by Tree-sitter's language bindings.

Features

  • Supports FASTQ files from various high throughput sequencers
    • Illumina X
    • ...
    • Roche Axelios 1
  • Syntax highlighting
    • Colours for all nucleobases
    • Record name and :-separated highlights in header lines

Get started

Install the grammar following your text editor's instructions or install the package for a supported programming language with Tree-sitter bindings. See Installation for details.

Other Tree-sitter grammars I've written:

These other projects have no affiliation with this one, but may be of interest:

  • tree-sitter-fasta: An alternative Tree-sitter grammar for FASTA files by Will Gebbie
  • sequed: DNA sequence editor and alignment viewer for Emacs by Bruce Rannala
  • bioSyntax: Syntax highlighting for computational biology in various text editors